Variant report

Variant	rs4075350
Chromosome Location	chr5:112373718-112373719
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112372620..112374480-chr5:112377239..112378903,2	K562	blood:
2	chr5:112368998..112372284-chr5:112372465..112374362,3	K562	blood:
3	chr5:112373432..112375747-chr5:112376830..112379641,2	K562	blood:
4	chr5:112372883..112375761-chr5:112416823..112419304,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10039618	0.80[JPT][hapmap]
rs10054158	0.81[CHD][hapmap];0.82[GIH][hapmap];0.81[EUR][1000 genomes]
rs1057474	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11749921	0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs12517398	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12654474	0.80[EUR][1000 genomes]
rs13156493	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs13159449	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13177101	0.92[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs13186334	0.92[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13445	0.85[CHB][hapmap];0.88[CHD][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1363333	0.82[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1549181	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17312754	0.81[EUR][1000 genomes]
rs17372511	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2112454	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2227948	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2416300	0.88[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs3185733	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs33544	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs33551	0.86[JPT][hapmap]
rs33552	0.81[JPT][hapmap]
rs33554	0.90[JPT][hapmap]
rs33557	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs33568	0.85[JPT][hapmap]
rs3857434	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4073358	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4073359	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4074190	0.81[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4301226	0.88[CHD][hapmap];0.85[JPT][hapmap]
rs4428399	0.88[ASN][1000 genomes]
rs4599529	0.81[CHD][hapmap];0.86[GIH][hapmap];0.80[EUR][1000 genomes]
rs4705529	0.84[EUR][1000 genomes]
rs4705744	0.87[EUR][1000 genomes]
rs4705745	0.80[EUR][1000 genomes]
rs4705749	0.92[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4705750	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705752	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705755	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4705756	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4705758	0.85[JPT][hapmap]
rs4705762	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs4778	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6594665	0.88[CHD][hapmap];0.85[JPT][hapmap]
rs6869100	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6877769	0.93[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs6893016	0.80[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.81[EUR][1000 genomes]
rs6893389	0.81[JPT][hapmap]
rs6894219	0.81[CEU][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6894937	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7670	0.87[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7701781	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7708603	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7732198	0.84[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap]
rs9122	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9784647	0.81[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv882717	chr5:112336588-112408944	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv15902	chr5:112369563-112410775	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv599395	chr5:112370311-112428869	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv1817377	chr5:112373682-112389837	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4075350	MCC	cis	Whole Blood	GTEx
rs4075350	DCP2	cis	lymphoblastoid	seeQTL
rs4075350	DCP2	cis	Skin Sun Exposed Lower leg	GTEx
rs4075350	MCC	cis	cerebellum	SCAN
rs4075350	TSLP	cis	parietal	SCAN
rs4075350	DCP2	cis	multi-tissue	Pritchard
rs4075350	DCP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112360000-112379000	Weak transcription	Small Intestine	intestine
2	chr5:112362800-112385800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:112363000-112374000	Weak transcription	Pancreas	Pancrea
4	chr5:112363600-112379000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr5:112363600-112379000	Weak transcription	Brain Substantia Nigra	brain
6	chr5:112363600-112379200	Weak transcription	Gastric	stomach
7	chr5:112363600-112379200	Weak transcription	Spleen	Spleen
8	chr5:112363600-112382800	Weak transcription	Fetal Intestine Small	intestine
9	chr5:112363800-112376200	Weak transcription	Dnd41	blood
10	chr5:112363800-112384600	Weak transcription	Aorta	Aorta
11	chr5:112363800-112386200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr5:112363800-112399000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:112363800-112409200	Weak transcription	Colonic Mucosa	Colon
14	chr5:112363800-112417800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr5:112364000-112374200	Weak transcription	HUVEC	blood vessel
16	chr5:112364000-112374600	Weak transcription	Lung	lung
17	chr5:112364000-112379000	Weak transcription	Fetal Lung	lung
18	chr5:112364000-112389400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr5:112364200-112386600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr5:112364600-112379000	Weak transcription	Brain Hippocampus Middle	brain
21	chr5:112364800-112378800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr5:112364800-112382800	Weak transcription	Fetal Intestine Large	intestine
23	chr5:112364800-112382800	Weak transcription	Fetal Thymus	thymus
24	chr5:112365600-112376400	Weak transcription	Primary T cells from cord blood	blood
25	chr5:112365800-112376800	Weak transcription	Thymus	Thymus
26	chr5:112365800-112382200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:112366600-112379200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr5:112367600-112378200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:112368800-112379400	Strong transcription	Fetal Stomach	stomach
30	chr5:112368800-112382800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr5:112369000-112379000	Weak transcription	Psoas Muscle	Psoas
32	chr5:112369200-112378800	Weak transcription	Fetal Heart	heart
33	chr5:112369200-112380200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:112369400-112377400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr5:112369400-112382800	Strong transcription	Liver	Liver
36	chr5:112369800-112378000	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr5:112370200-112379200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr5:112370200-112406600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr5:112370600-112382800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:112370600-112396600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:112371000-112374400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:112371000-112383400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr5:112371200-112373800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:112371200-112373800	Weak transcription	NHEK	skin
45	chr5:112371200-112374000	Weak transcription	Osteobl	bone
46	chr5:112371200-112374400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr5:112371200-112374400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:112371200-112378600	Weak transcription	Right Atrium	heart
49	chr5:112371400-112373800	Weak transcription	NHDF-Ad	bronchial
50	chr5:112371400-112374000	Weak transcription	Muscle Satellite Cultured Cells	--

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